To estimate the long-term, persistent effects of missionary education requires two strong assumptions: that mission station settlement is uncorrelated with other economic variables, such as soil quality and access to markets, and 2) that selection into (and out of) mission stations is unimportant. Both these assumptions are usually not sufficiently addressed, which renders the interpretation of the persistent effects of mission stations suspect. We use an 1849 mission census of the Cape Colony in South Africa to test whether, controlling for location and selection, mission station education can explain education outcomes 147 years later. Our first set of results show that Black and Coloured residents of districts with a mission station are today likely to attain more years of schooling than those in districts with no stations. In addition, when only modern-day controls are included, education seems to be the mechanism that explains this persistence. However, when we control for selection in 1849, literacy loses its explanatory power. Education outcomes may be highly persistent – even in the face of active repression by apartheid authorities – but the key factor is early selection and not education persistence.